This repository contains a collection of pipelines that aid the analysis of single cell sequencing experiments. Currently there is one pipeline implimented that allows the analysis of drop-seq and 10X sequencing analysis. Current pipelines in development: 1) velocyto pipeline 2) smart-seq2 pipeline.
The preferred method for installation is through conda. Currently this installation is still in working progress. Preferably the installation should be in a seperate environment::
conda create -n single-cell -c cgat single-cell
conda activate single-cell
single_cell --help
The respository can also be installed manually, but dependancies will need to be installed seperately::
python setup.py install
single_cell --help
Run the single_cell --help command view the help documentation for how to run the single-cell repository.
To run the main single_cell droplet based pipeline run first generate a configuration file::
single_cell singlecell config
Then run the pipeline::
single_cell singlecell make full -v5
Then to run the report::
single_cell singlecell make build_report
Further help that introduces single-cell and provides a tutorial of how to run example code can be found at read the docs